There are a couple reasons you might see tweets in a snapshot report that don't show up in a Tracker.
1) Check the dates. Snapshot reports - both the free and the full versions - analyze tweets from the past few days. Trackers find and analyze tweets in real time. So, depending on when you ran the report and set up the Tracker, you might be looking at two different sets of tweets.
2) Reports use the public Twitter Search API and Trackers use the full-fidelity commercial data stream. In some rare cases, these APIs handle tweets differently. The Search API is less robust than the commercial stream.
3) Tracker search queries need to be very literal. This includes punctuation (more details here about writing Tracker queries). Some snapshot queries handle punctuation less literally, so you might get more results for a report search query with punctuation. Our best advice to get around this is to test your queries first with a free snapshot. And in Trackers, user quotation marks around your queries with punctuation to be sure we find exactly what you're looking for.
If you ever have questions about the data in your snapshots or Trackers, please ask us! Twitter changes small things all the time, and we do our best to stay up-to-date on how things work at any given point, so we're happy to help you figure it out.